Transcript Unit 1 - OpenWetWare

UNIT 1
Biotechnology and Microbiology
Definition Biotechnology

Biotechnology is broadly defined as the science of
using living organisms or the products of living
organisms for the benefit of humans and their
surroundings.
Biotechnology
The Biotechnology Revolution - NOVA
 http://www.youtube.com/watch?v=bukTqyWgaM8
Lesson 1
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
Lecture and Discussion: Introduction to classical and
modern biotechnology, interdisciplinary nature of
biotechnology, and ethics in biology.
Assessment: Create a concept map from lecture.
History of Biotechnology
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What is the difference between
classical biotechnology
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and modern biotechnology?
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Classical biotechnology
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Our ancient ancestors used two classic
biotechnology techniques:
Fermentation – use of microorganisms to make
food and beverages.
Selective Breeding – breeding of animals and
plants with desirable traits.
Fermentation
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Do you remember this?
http://people.cst.cmich.edu/schul1te/animations/fermentation.
swf
Fermentation
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Actual existence of micro-organisms and their role in contaminating
food are recent discoveries, dating back 200 years ago.
Bread baking
- Earliest breads were unleavened (pita bread).
- Fermented dough probably discovered by accident.
- Egyptians and Romans both used fermented dough to make a
lighter, leavened bread.
Fermentation
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Lactic Acid and Acetic Acid Fermentation
5,000 BC, milk curd to make cheese was made in
Mesopotamia.
By 4,000 BC, Chinese used fermentation to make yogurt,
cheese, and vinegar.
Fermentation
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Beverages
Beer Making
- Egyptians probably began beer making around
6,000 BC.
- Babylonians used barley to make beer.
- Brewing became an art form by the 14th century
AD.
Wine making
- Originated in valley of the Tigris River, date
unknown.
- First made by accident with grapes contaminated
by yeast.
- Egyptians, Greeks, and Romans made wine.
Selective Breeding
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About 10,000 years ago, people established agrarian societies.
Origins of biotechnology date back to this time.
People settled and began domesticating both animals and plants.
Both animals and plants, were artificially selected for valuable
traits.
Selective Breeding

Animals
- Babylonians, Egyptians, and
Romans selectively bred
livestock.
- Romans have left written
descriptions of their livestock
selective breeding practices.
- British white cattle (on right)
can trace its ancestry back to
the Roman empire.
Selective Breeding
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Plants
- Superior seeds, cuttings, and
tubers have been selected for
thousands of years to save for the
next planting.
- Sumarians, Egyptians, and
Romans collected and traded
superior seeds and plants.
- (On right) Evolutionary changes
in corn from 5,000 BC to 1,500 AD
in Mexico.
Modern Biotechnology
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Advances in genetics and molecular biology have
led to innovations and new applications in
biotechnology.
Classical biotechnology took advantage of natural
microbial processes or artificially selected
phenotypes. Genetics of these selected organisms
proceeded naturally.
Modern biotechnology uses
- Genetic Engineering
- Gene Cloning
Modern Biotechnology

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Genetic Engineering Ability to manipulate DNA of
an organism. Manipulation
due to Recombinant DNA
Technology. Recombinant
DNA technology combines
DNA from different sources.
Gene Cloning –
The ability to identify and
reproduce a gene of interest.
Modern Biotechnology
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Recombinant DNA technology has
dominated modern biotechnology.
Has led to:
- Production of disease resistant
plants.
- Genetically engineered bacteria to
degrade environmental pollutants and
to produce antibiotics.
Gene cloning and recombinant DNA
technology have impacted human
health through the Human Genome
Project.
Discussion questions
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What are the differences between classical and
modern biotechnology? Be sure to discuss the
processes involved
Discuss the differences with a partner.
Class discussion will follow.
Biotechnology – A science of many
disciplines

What disciplines contribute to the science of
biotechnology?
Biotechnology – A science of many
disciplines.
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The roots of biotechnology are formed by:
- Human, animal, and plant physiology
- Mathematics
- Molecular and cell biology
- Immunology
- Statistics
- Microbiology
- Biochemistry
- Genetics
- Physics
- Chemical Engineering
- Computer Science
Biotechnology- A science of many
disciplines

The “root” subjects pieced
together can lead to genetic
engineering approached with
applications in:
- Drug development
- Environmental and Aquatic
Biotechnology
- Agricultural Biotechnology
- Forensics and Detection
- Medical Biotechnology
- Regulatory Approval and
Oversight.
Biotechnology – A science of many
disciplines

A typical example of interdisciplinary
nature of biotechnology.
- Scientific microbiology research discovers
a gene or gene product of interest.
- Biochemical, molecular, and genetic
techniques are used to determine the role of
the gene.
- Bioinformatics (computer data bases) are
used to study gene sequence or analyze
protein structure.
- Gene then used in a biotechnology
application.
Ethics in Biotechnology
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What are the ethical concerns in biotechnology?
Ethics in Biotechnology
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Powerful applications and potential promise of biotechnology raises
ethical concerns.
Not everyone is a fan of biotechnology.
The wide range of legal, social, and ethical issues are cause for
debate and discussion among scientists, the general public, clergy,
politicians, lawyers, and many others.
Some questions of concern:
- Should human cloning be permitted?
- Will genetically modified foods be harmful to the environment?
- Should we permit the development of synthetic genomes?
Ethics in Biology
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
We will be looking at
and discussing some of
the ethical concerns in
biotechnology.
Our goal is not to tell
you what to think but to
empower you with the
knowledge you can use to
make your own wise
decisions.
Discussion questions
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What is a typical example of biotechnology as an
interdisciplinary science?
What is bioinformatics?
What is our goal with respect to making ethical
decisions about biotechnology?
Create a Concept Map
Read how to create a concept map.

http://www.libraries.psu.edu/psul/lls/students/research_resources/conceptmap.html
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Create a concept map which incorporates the following terms:
Agricultural biotechnology
Animal
Applications
Beverage making
Biochemistry
Bioinformatics
Biotechnology
Bread making
Classical biotechnology
Computer Science
DNA recombinant technology
Drug development
Environmental biotechnology
Ethical
Fermentation
Forensics
Gene cloning
Genetic engineering
Immunology
Interdisciplinary science
Issues in biotechnology
Lactic/acetic acid fermentation
Legal
Medical biotechnology
Microbiology
Molecular biology
Plant
Root sciences
Selective breeding
Social
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Lesson 2
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Case Study : A Glimpse into the Futre
Start by viewing the video: http://bigthink.com/ideas/16344
Read case study: “ A Glimpse into the Future,” by Lee Silver a
molecular biologist at Princeton University.
Work in groups of 4 students and discuss the focus questions: What
arguments does Silver give for thinking that human genetic
enhancement be regarded as morally permissible? What arguments
are used by opponents of genetic enhancement?
Complete: Student self and group evaluation of group participation
Whole class discussion: How we make ethical decisions, as well as
any points of clarification needed by students.
Write an individual persuasive 5 paragraph essay supporting your
opinion on use of genetic enhancement.
Lesson 2 – Work Groups Term 1

A Framework for Ethical Decisions
1. Recognize an Ethical Issue
 Could this decision or situation be damaging to
someone or to some group? Does this decision
involve a choice between a good and bad
alternative, or perhaps between two "goods" or
between two "bads"?
 Is this issue about more than what is legal or what is
most efficient? If so, how?
A Framework for Ethical Decisions
2. Get the Facts
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What are the relevant facts of the case? What facts
are not known? Can I learn more about the situation?
Do I know enough to make a decision?
What individuals and groups have an important stake
in the outcome? Are some concerns more important?
Why?
What are the options for acting? Have all the relevant
persons and groups been consulted? Have I identified
creative options?
A Framework for Ethical Decisions
3. Evaluate Alternative Actions
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Evaluate the options by asking the following questions:
Which option will produce the most good and do the least harm?
(The Utilitarian Approach)
Which option best respects the rights of all who have a stake? (The
Rights Approach)
Which option treats people equally or proportionately? (The Justice
Approach)
Which option best serves the community
as a whole, not just some members?
(The Common Good Approach)
Which option leads me to act as the sort of person I want to be?
(The Virtue Approach)
A Framework for Ethical Decisions
4. Make a Decision and Test It
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Considering all these approaches, which option best
addresses the situation?
If I told someone I respect-or told a television
audience-which option I have chosen, what would
they say?
A Framework for Ethical Decisions
5. Act and Reflect on the Outcome
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How can my decision be implemented with the
greatest care and attention to the concerns of all
stakeholders?
How did my decision turn out and what have I
learned from this specific situation?
Lesson 3
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Individually read the Powerpoint slides for lesson 3 and respond to the
questions.
Create 7 groups.
Each group will be assigned one of the following topics and a
corresponding article:
1. Microbial Biotechnology 2. Agricultural Biotechnology
3. Animal Biotechnology
4. Forensic Biotechnology
5. Bioremediation
6. Marine Biotechnology
7. Medical Biotechnology
Read the article and work together to create an accurate summary of the
article
One member from each group will then present their assigned section of
the powerpoint and provide a summary of their article. Write your article
title on the whiteboard.
Microbial Biotechnology
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1.
2.
Microbes have been used in many
ways that affect society.
Manipulating microbial DNA has
created organisms that manufacture
food.
Manipulated microbes are used to
make
- enzymes
- vaccines
- antibiotics
- insulin and growth hormones
- detectors for bioterrorism
- decontamination processes for
industrial waste.
Agricultural Biotechnology
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Plants have been bioengineered
for
- Drought resistance
- Cold tolerance
- Pest resistance
- Greater food yield
Plants have been used for molecular
pharming. Plants are
bioengineered to produce
recombinant proteins.
Downside: Gene transfer from
engineered plants to non- target
plants in the environment has
produced some super weeds.
Animal Biotechnology
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Goats, cattle, sheep, and chickens are
being used to produce antibodies and
other medically needed proteins.
Transgenic animals become bioreactors.
They contain genes from another sources
and produce these proteins in their milk.
Animals are used in “knockout”
experiments. Genes are disrupted and
much is learned about gene function.
Many animals have been cloned; possible
uses for using cloned animals for
genetically engineered organs have been
explored.
Forensic Biotechnology
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DNA fingerprinting, methods to detect unique DNA
patterns are being used in:
- Law enforcement
- Paternity testing
- Poaching of endangered species
- Tracking AIDS, Lyme disease, West Nile virus, TB.
- Testing of food products to see if food substitutes
are being used.
Bioremediation
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Microbial processes are
used to degrade natural
and man made
substances.
Bioremediation is used
in the clean up of massive
oil spills; cleans up
shorelines three times
faster than traditional
clean up methods.
Marine Biotechnology
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Aquaculture – raising fish or
shellfish in controlled conditions to
use as food sources.
- Genetically engineered disease
resistant oysters
- Vaccine against viruses that infect
fish
- Transgenic salmon injected with
growth hormone that have
extraordinary growth rates.
Bioprospecting – Identifying marine
organisms with novel properties to
exploit for commercial purposes.
Ex. Snails are a rich source of antitumor molecules.
Medical Biotechnology
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New drugs and vaccines have
been developed.
Human Genome Project is helping
to identify defective genes and in
the creation of new genetic tests.
Gene Therapy – Inserting normal
genes into a patient to replace
defective ones.
Stem Cell Technology – Possible
use in the development of new
tissues to replaced damaged
tissues.
Lesson 4
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View the video “Microbial Evolution” and respond
to student worksheet
Lecture: Species Concept and Evolutionary
Domains. Response to questions.
Lecture: Phenotypic Classifcation. Complete
Powerpoint review of lecture
At the end of the lesson, write for 2 minutes about
what you learned in Lesson 4.
Microbial evolution
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http://www.youtube.com/watch?v=XawzIjX72U0
http://www.youtube.com/watch?v=YPgxEl9jzRU&featu
re=relmfu
http://www.youtube.com/watch?v=aF5sLLLalm8&featur
e=relmfu
http://www.youtube.com/watch?v=vghlsa7oD_8&featu
re=relmfu
4 parts of video
Lesson 4
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What is a species?
A species is defined as a
population that can naturally
interbreed and produce fertile
offspring, and that is
reproductively isolated from
other species.
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Right!
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Well, maybe not……..
Species Concept - Microbiology
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A bacterial species is a
prokaryote whose 16S ribosomal
RNA sequence differs by no more
that 3%.
http://www.microbeworld.org/car
eers/tools-of-the-trade/genetictools-and-techniques/16s-rrna
That is, at least 97% of the rRNA
sequence is identical in a bacterial
species.
A bacteria whose rRNA differs by
more than 3% usually turns out to
be a different species.
Species Concept- Microbiology
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Prokaryotes do not fit the biological species concept
because they are haploid and reproduce asexually.
They cannot produce “fertile offspring” like plants and
animals can.
In microbiology, evolutionary (molecular)chronometers
measure evolutionary change.
In other words, differences in nucleotide or amino acid
sequences of functionally similar (homologous)
macromolecules are a function of their evolutionary distance.
The greater the number of differences in a sequence the
more distantly related the two species are.
Species Concept - Microbiology
Molecular Chronometers
 The chronometer must be present in all groups
being classified and it must be functionally
homologous (not many sequence differences).

The following genes and proteins are most
frequently used to classify bacteria.
- ribosomal RNA
- ATPase proteins (synthesize ATP) 
- RecA (enzyme facilitates genetic
recombination)
- Certain translation proteins.

Species Concept- Microbiology
Ribosomal RNA is the most
widely used chronometer for
identifying bacterial species :
- It is relatively large.
- Universally distributed
- Has many nucleotide sequences
that are conserved.
 16S rRNA are part of the small
subunit (SSU) of the ribosome;
used to classify prokaryotes.
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Evolutionary Tree - Microbiology
Phylogenetic Tree of Life - rRNA
Three Domains - Microbiology
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Bacteria
At least 40 phyla of bacteria
in this domain.
Most of the phyla are related
from a phylogenetic standpoint
but have little in common in
terms of phenotype.
Proteobacteria contain species
which are the ancestors of
mitochondria.
Three Domains - Microbiology
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Archaea
4 phyla in this domain
Contain extremophiles
- Hyperthermophiles: live in
high temperatures.
- Methanogenic : produce
methane.
- Extreme halophiles: live in
high salt environments.
Contains Ignicoccus, bacteria with
the smallest genome.
Three Domains - Microbiology
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Eukarya
rRNA phylogeny based on
18S rRNA.
Four kingdoms: Protista, Fungi,
Plant, and Animal.
Range from single cell to
complex multi-cell organisms.
Rapid diversification of
Eukarya was tied to changes in
oxygen levels on earth.
Phenotypic Classification-Bacteria
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Working microbiologists use phenotypic
commonality in identifying bacteria. Most
frequently these phenotypes are:
Cell shape
Cell wall structure
Cell respiration
Growth factors
Colony morphology
Phenotypic Classification-Bacteria
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Cell Shape
There are 4 bacterial shapes:
- Cocci (coccus s.) or round
- Bacilli (bacillus s.) or rod shaped
- Spirillum or cork screw shaped
- Filamentous or like jelly beans in straw
Phenotypic Classification- Bacteria
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Cocci
Round shape
Examples
-Staphlococcus 
(in clusters)
-Streptococcus
(in chains) 
Phenotypic Classification - Bacteria
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Bacilli
Rod shaped
Examples
- Bacillus anthracis 
(agent in anthrax)
- Escherichia coli 
(used in biotechnology)
Phenotypic Classification- Bacteria
Spirillum
 Cork screw shape
 Example
- Treponema pallidum
(agent of syphilis)
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Phenotypic Classification-Bacteria
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Filamentous
Jelly beans in straw
Example
-Leptothris discophora
(aquatic bacteria uses
iron the way we use
oxygen).
Phenotypic Classification -Bacteria
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Composition of Cell Walls
Difference in cell wall structure becomes clear when a
technique called the Gram stain is used.
Bacteria on a glass slide are stained first with a
purple dye; the slide is rinsed with ethanol, and then a
red counter stain is applied.
If bacteria remain purple = Gram positive.
If bacteria turn red = Gram negative.
http://www.youtube.com/watch?v=Qk2OjqatCqc&f
eature=related
Phenotypic Classification-Bacteria
 Gram + cocci
Gram – rods 
Phenotypic classification
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All bacteria have a cell membrane and a cell wall
composed of peptidoglycan.
Phenotypic Classification-Bacteria
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Gram positive bacteria have their cell membrane and a simple but thick cell
wall of peptidoglycan . Peptidoglycan gives shape to the cell.
Gram negative bacteria have their cell membrane and a thinner layer of
peptidoglycan plus an outside layer of lipopolysaccharides.
Lipopolysaccharides make gram negative organisms more threatening than
gram positive organisms.
Phenotypic Classification-Bacteria
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Cell Respiration
There are 3 types of cell respiration( synthesis of
ATP):
- Aerobic: Use oxygen for cell respiration.
- Anaerobic: Cannot tolerate oxygen. Use
fermentation
- Facultative anaerobes: Can use or not use
oxygen depending on availability.
Phenotypic Classification-Bacteria
Growth Factors
 Nutrient Source
- Heterotroph: Consume energy from outside
source.
- Autotroph: Make and consume energy.
 Energy Source (Autotrophs)
- Chemoautotroph : Use chemicals as energy
source.
- Phototrophs: Use light as energy source.
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Phenotypic Classification-Bacteria
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Colony morphology
A single bacteria put onto
a solid agar plate, if given
sufficient nutrients, optimal
temperature and pH, will
multiply and form a colony.
All members of the colony
are genetically identical.
Bacterial colonies of
different species differ from
one another.
Phenotypic Classification-Bacteria
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To identify a colony, the following basic elements are
noted.
Form- What is the basic shape of the colony?
Elevation - What is the cross sectional shape of the colony?
Margin - What is the magnified shape of the edge of the
colony?
Surface - How does the surface of the colony appear?
Opacity – Is the colony translucent, transparent, iridescent?
Chromogenesis – pigmentation.
Phenotypic Classification
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Form - Shape of the colony
Phenotypic Classification- Bacteria
• Elevation – Cross sectional shape
Phenotypic Classification-Bacteria
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Margin - Shape of the colony edge.
Phenotypic Classification-Bacteria
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Opacity – Clear, Opaque, Iridescent
Iridescent
Phenotypic Classification
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Chromogensis - Pigmentation
Lesson 5
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Visit the 3 websites noted on your handout to learn
about prokaryotic structures and function.
Respond to all questions.
Next read the Powerpoint slides on prokaryotic
structure and respond to all questions.
Prokaryotic structure
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DNA in prokaryotes
DNA is found in the
- Nucleoid Region
- Plasmids
A typical prokaryote has one
chromosome containing most of the genes
in the cell.
A few species of Bacteria & Archaea
contain two chromosomes.
The DNA is a double stranded circular
molecule.
Bacterial genomes contain from
500,000 base pairs to about 4 million
base pairs, depending on the species..
Prokaryotic Structure
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Plasmids
Plasmids are genetic elements (DNA) that
exist and replicate separately from the
chromosome.
Most are circular, some are linear.
Many prokaryotes contain one or more
plasmids.
They range in size from 100 to 1,000 base
pairs.
Plasmid DNA can be exchanged among
bacteria.
For example, genes for antibiotic resistance
are found on plasmids and one bacteria can
transfer these genes to another bacteria.
Bacterial plasmids play a role in recombinant
DNA technology.
Prokaryotic Structure
The differences between a bacterial chromosome
and a plasmid:
- Chromosomes carry many more genes than
plasmids and the genes are essential to cellular
function. Essential genes are called housekeeping
genes.
- Plasmids carry far fewer genes and are
expendable because the genes are not necessary
for growth under all conditions.
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Prokaryotic Structure
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Restriction Endonucleases (Enzymes)
Are naturally found in bacteria.
When viruses invade bacteria, restriction
endonucleases have the ability to cut up
the foreign viral DNA. The possibility of
viral infection plummets.
Can be thought of as a bacterial immune
system because the role of restriction
endonucleases is to protect the bacteria.
Bacteria can have more than one type
restriction enzymes.
Bacterial restriction enzymes play a role
in recombinant DNA technology.
Lesson 6
Lab experiment to demonstrate effectiveness of antimicrobial soap.
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Lab:
- Review the following videos for instruction in microbiological techniques.
http://www.youtube.com/watch?v=PiWwnBbCrNs&feature=related
Pouring agar plates.
http://www.youtube.com/watch?v=zZ1NQau1wtw
Dilutions and spread plating
http://www.youtube.com/watch?v=AaG3Pt3nwLQ&feature=relmfu
Streaking plates
http://www.youtube.com/watch?v=tBmNitxvqyc
Aseptic transfer
http://www.youtube.com/watch?v=SLkipIg4WRg
Making smears
http://www.youtube.com/watch?v=-j97pZo5t4g&feature=related
Gram stains
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Lab
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Day 1: Handwashing and plate innocculation
Day 2: Review Streaking for isolation video, collect
data, and streak plates for isolation
Day 3: Collect data, study colony morphology,
and gram stain
Lesson 7
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E.coli
Lecture:
- E.coli the organism and its use in biotechnology.
- Pathogenic E. coli
Read handout on pathogenic E.coli. Respond to
questions. Class Review
Case Study “Microbial Pie”
Track the Epidemic
E.coli
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Escherichia coli
Gram negative rod normally
found in the intestines of
warm blooded animals.
E.coli can benefit its host by
producing vitamin K and by
reducing numbers of
pathogenic bacteria in the
intestine.
E. coli
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E.coli is a hardy organism that is
easy to culture and easy to
manipulate in the lab.
It is a model organism in
biotechnology.
Model organisms are extensively
studied to understand biological
phenomena and the information
can be applied to other
organisms.
E.coli genome was one of the first
to be sequenced in 1997.
E.coli
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Most economically robust
area in biotechnology is
production of human proteins.
E.coli has played a major
role in production of these
proteins.
Human genes for proteins
can be cloned and inserted
into plasmids in E.coli through
recombinant DNA technology
E.coli
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E.coli is then grown in large
bioreactors and it produces the
protein of interest.
Purification methods
separate the target protein
from the biological molecules in
which it was produced.
The proteins can then be used
by humans.
E.coli
The following proteins are
manufactured via this
technique:
Insulin
For diabetes
Human Growth Hormone
For growth hormone deficiency
Factor VIII
For hemophilia
Erythropoietin
For stimulation RBC growth
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E. coli
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Pathogenic vs. Non-pathogenic
E.coli.
Most E.coli strains live commensally
in the intestines of warm blooded
animals. These strains are nonpathogenic.
Non-pathogenic strains of E.coli
strains are used in biotechnology
research.
Some E.coli strains are virulent and
produce gastrointestinal disease.
These strains are pathogenic.
E. coli
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Causes of virulence
Toxicity
- Ability to cause disease by a preformed toxin.
Toxin inhibits host cell function and kills host cell.
Invasiveness
- Ability of organism to grow in host cell tissue in
such large numbers that pathogen inhibits host cell
activity.
E. coli
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E.coli virulence
Due to an enterotoxin, a type of
exotoxin.
The enterotoxin is secreted by the
bacteria and affects the cell
membrane of intestinal cells.
It makes the host cell membrane
more permeable to chloride ions. As
chloride enters the host cells, sodium
and water leave the host cells.
This causes diarrhea and abdominal
pain.
Virulent E.coli is acquired by eating
contaminated food.
Lesson 8
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Lecture: Natural gene transfer and recombination.
Whole class lecture: Gene transfer in prokaryotic
organisms.
Pantomime of gene transfer
Case Study: Antibiotic resistance
Read each section of case study. Respond to questions.
In between each section of the case study, the whole class
will have a discussion to clarify any of your concerns.
Gene Transfer and Recombination



1.
2.
3.

Bacteria pass on their genetic material to the next
generation asexually through binary fission.
Many bacteria, however, have the capacity to physically
exchange genetic material with other bacteria.
There are 3 processes in which genetic material can be
exchanged:
Transformation
Transduction
Conjugation
These 3 process are collectively referred to as lateral or
horizontal gene transfer.
Gene Transfer and Recombination


Transformation
Is a process by which free DNA is incorporated into
a recipient cell and brings about genetic change.
Gene Transfer and Recombination
Do you remember the Griffith experiment?
http://science.jburroughs.org/mbahe/BioA/starranimation
s/chapter8/videos_animations/griffith.html

Gene Transfer and Recombination







Transformation
If a bacterial cell is lysed, the DNA pours
out.
The bacterial chromosome then breaks apart
into fragments with about 10 genes on them.
Other bacterial cells that are competent can
take up the DNA from the environment.
Competency is genetically determined.
The DNA enters the cell and is escorted
through the cytoplasm by competence specific
proteins to prevent degradation.
DNA is then recombined (integrated) into the
bacterial chromosome.
http://highered.mcgrawhill.com/sites/0072556781/student_view0/c
hapter13/animation_quiz_1.html
Gene Transfer and Recombination





Transformation in
Biotechnology
In biotechnology procedures,
the term transformation has a
slightly different meaning.
E.coli are poorly transformed
under natural conditions.
If you treat the organism with
calcium ions and chill it, it
becomes easily transformed.
Transformation of this organism
generally occurs in the plasmid.
Gene Transfer and Recombination


Transduction
DNA is
transferred from
cell to cell by a
virus. Virus can
transfer host cell
DNA along with
its own genetic
material.
Gene Transfer and Recombination





In transduction, any gene on a donor bacterial chromosome
can be transferred to a recipient.
A phage (virus for bacteria) enters the host cell and during
a lytic infection enzymes responsible for packaging viral
DNA sometimes package the host DNA accidentally.
The resulting virus with a piece of the donor DNA is called
a transducing particle.
This transducing particle cannot go on to cause infection in
a new cell. The DNA released is incorporated into a
recipient bacterial cell chromosome.
http://highered.mcgrawhill.com/sites/0072556781/student_view0/chapter13/ani
mation_quiz_2.html
Gene Transfer and Recombination

Transduction
Gene Transfer and Recombination








Plasmids revisited
Before we learn conjugation, let’s review plasmids.
Plasmids:
Are genetic elements that replicate independently of the host
chromosome.
Are unessential, do not control vital cell functions.
Are double stranded, mostly circular (some linear), structures with
fewer genes than the bacterial chromosome.
Of different types may be present in a cell and numbers of these
types can vary.
Called episomes can integrate into the bacterial chromosome.
Gene Transfer and Recombination






Types of plasmids
F (fertility) plasmid - most studied, results in the
expression of sex pili.
R (resistance) plasmids - contain genes that can
build a resistance against antibiotics
Col plasmids - which contain genes that code for
bacteriocins that can kill other bacteria.
Degradative plasmids, which enable the
digestion of unusual substances.
Virulence plasmids- which turn the bacterium
into a pathogen.
Gene Transfer and Recombination




Conjugation
Is a process of genetic transfer
that involves cell to cell contact.
A conjugative plasmid uses this
process to transfer a copy of
itself to a new host.
The process involves a donor
cell and a recipient cell.
Gene Transfer and Recombination



Conjugation (using
the F plasmid as an
example)
The F+ cell has the
plasmid and the
ability to donate it.
(donor)
The F- cell is the
recipient.
Gene Transfer and Recombination



Conjugation
F+ cell synthesizes a
sex pillus.
Sex pillus makes
specific contact with
the F- cell; pulling it
toward the F+ cell.
Gene Transfer and Recombination



Conjugation
The DNA (plasmid) is
transferred from the F+ to
the F- cell through the sex
pillus.
Depending on the species,
sometimes the plasmid is
replicated first in the F+
cell and then transmitted to
F-. Other times, the 2 DNA
strands are separated in F+
and one strand is
transferred to F-. Both cells
will then make a
complimentary strand..
Gene Transfer and Recombination




The original F- cell turns into an F+ cell and can
conjugate with other bacteria.
Conjugative plasmids can spread rapidly through
populations much like infectious agents.
If plasmids contain genes that offer a selective
advantage (like an antibiotic resistance gene), this can
ensure survival of that population.
http://highered.mcgrawhill.com/sites/0072556781/student_view0/chapter13
/animation_quiz_3.html
Think-Pair-Share


Work with a partner and explain transformation,
transduction, and conjugation to your partner.
Exchange places and have your partner explain the
same to you.
Gene Transfer and Recombination





Create 6 groups
We will create pantomimes
of horizontal gene transfer.
2 groups – Transformation
2 groups- Transduction
2 groups - Conjugation
Lesson 9









Products of microbial biotechnology
For homework read and familiarize yourself with the Powerpoint.
Read each article on the website at the bottom of each slide and make a copy
of it for your notes.
Class Review: You will be assigned one of the articles and you will have to
write an abstract of the article on the following day in class.
Genetically modified foods
Work with a partner and read research articles on genetically modified foods.
Discuss the pros and cons of the argument with partner.
Work in groups of 4 on assigned topic. Research on computer additional
information to support your topic. Develop a 5 minute argument defending
your position.
Debate: One person from each group will present pro or con argument.
Instead of rebuttal, each student will have to speak for 1 minutes about their
opinion on genetically modified food. Class will vote at end of debate.
Products Microbial Biotechnology
Food Biotechnology - fermentation
 We have discussed fermentation of foods.
 Scientists are currently working on ways to improve microorganisms for food production.
- Developing virus resistant organisms through recombinant
DNA technology to prevent economic losses in the dairy
industry.
- Developing bacteria to produce chemicals to kill
contaminating organisms in food making processes.
- Produced a microbial enzyme used to make cheese.
http://www.gmocompass.org/eng/grocery_shopping/processed_foods/29.
dairy_products_eggs_genetic_engineering.html

Products Microbial Biotechnology
Enzymes, Antibiotics, and Human Proteins.
 Recombinant DNA technology has enabled production of new
enzymes, antibiotics, and human proteins from microbial
fermentation.
 Prourokinase is an enzyme which helps heal wounds infected
with E.coli.
 New and novel antibiotics with two pathways for treatment are
being developed.
 Tissue plasminogen activator, a protein which dissolves blood
clots is being produced.
 Read about biotechnology and detergents.
http://www.biotecharticles.com/Biotechnology-productsArticle/Biotechnology-in-the-Manufacturing-of-Detergents159.html

Products Microbial Biotechnology



Fuels and Biopolymers
Hydrogen power is a fuel of the future. Biotechnologists
are looking at Clostridium species as generators of
hydrogen.
Plastics worldwide are polluters because they are not
biodegradable. Several organisms are being studied as
producers of bioplastics. These biodegradable plastics will
have several applications in the industrial and medical
fields. http://news.softpedia.com/news/Bacteria-ConvertsVegetables-to-Bioplastic-167546.shtml
Products Microbial Biotechnology



Agriculture
A Pseudomonas bacteria has been bioengineered with
B. thuringiensis toxin . The bacteria colonizes plants and
acts as a biopesticide to kill insect larvae.
Baculoviruses are used to contaminate plant material.
Insects ingest the plant and develop a lethal viral
infection Biotechnologists are working on ways to
bioengineer the Baculovirus to enhance its ability as a
biopesticide.
http://www.biocontrol.entomology.cornell.edu/pathoge
ns/baculoviruses.html
Products Microbial Technology




Bioremediation
Microorganisms with hydrocarbon oxidizing enzymes
clean oil spills.
Microorganisms are used in waste water treatment
facilities to purify water.
Bacteria are being studied which have the capacity to
remove heavy metals such as arsenic, copper, tin, and
mercury from the environment.
http://freshscience.org.au/2003/aussie-arsenic-eatingbacteria-may-save-lives-and-clean-mines
Lesson 10

Lecture and discussion: Eukaryotic microbes and
biotechnology products.
Lesson 10 Eukaryotic Cells




Eukaryotic cell review: Review structure & function,
sketch a eukaryotic cell, and trace the pathway of
lipoprotein assembly.
Lecture: Yeast, Fungi, and Biotechnology products.
Video: The Biology of Fungi (16 min)
Reading and response: Evolutionary ties of fungi.
Microbial Eukaryotic Cells


http://www.biologyjunction.com/cell_functions.htm
Review of basic eukaryotic cell
Microbial Eukaryotic Cells








Fungi – General Characteristics
Fungi are composed of eukaryotic cells.
Some are unicellular and some are multicellular.
Habitats: Most are terrestrial and some are
aquatic
Energy : Fungi are heterotrophic decomposers.
(A few are parasitic)
Cell Walls: Resemble plants architecturally but
are made of chitin not cellulose.
Reproduction: Many reproduce asexually and
sexually using spores.
Recent molecular evidence suggests fungi are
probably more closely related to animals than to
plants or protists. http://www.fungionline.org.uk/
Microbial Eukaryotic Cells

a.
b.
c.
There are 3 basic types
of fungi
Unicellular fungi - Yeast
Filamentous fungi –
Mold and fungi
Macroscopic fungi –
Mushrooms
We will limit our discussion to
the first two types.
Microbial Eukaryotic Cells
Yeast

There are 1,500 species of
yeast and yeast are not part of a
single taxon.

Cells
- typically spherical, oval, or
cylindrical
- usually 3-4 microns in size
- most are unicellular
- some multicellular: a string of
connected yeast cells connected
by psuedohyphae.

Microbial Eukaryotic Cells


Yeast with
pseudohyphae
Pseudohyphae help
yeast invade tissues.
Microbial Eukaryotic Cells

Yeast colonies
growing on
agar.
Microbial Eukaryotic Cells




Energy
Yeast flourish in
environments where sugar
is present.
They are facultative
aerobes; using aerobic
cell respiration and
fermentation.
In a lab, yeast can be
cultured with nutrient agar
and grow colonies.
Microbial Eukaryotic Cells



Reproduction
Yeasts generally
reproduce asexually
by budding.
http://www.youtube
.com/watch?v=iOvr
q6ssy2Y
Microbial Eukaryotic Cells






Reproduction
Yeast can sexually reproduce
by mating.
Two different mating types
fuse into a diploid cell.
Diploid cell can bud to make
additional diploid cells.
Diploid cell undergoes meiosis
and produces haploid cells
called ascospores.
Ascospores create new yeast
cells.
Microbial Eukaryotic Cells

Yeast containing
ascospores.
Review
What are the general characteristics of fungi?
 Name the 3 types of fungi and provide an
example.
 Describe the following:
1. Structure of yeast
2. Energy use in yeast
3. Asexual and sexual reproduction of yeast

Microbial Eukaryotic Cells



Filamentous
Fungi
Widespread in
nature, usually
seen on stale
bread, cheese, or
fruit.
Called molds.
Microbial Eukaryotic Cells




Cell Structure
A filament called a hypha
(hyphae p,) grows from a
single terminal cell.

The hyphae grow together
across a surface and form
compact tufts called
mycelium.
This compact mat
represents many intertwined
hyphae. 
Microbial Eukaryotic Cells





Cell Structure
From the mycelium,
hyphae grow upward.
At the end of the vertical
hyphae are spores called
conidia.
Conidia are asexual
spores and are often
pigmented.
http://bugs.bio.usyd.edu.
au/learning/resources/C
AL/Microconcepts/Repro
duction/fungiRepro.html
Microbial Eukaryotic Cells



Reproduction
(asexual)
The function of the
conidia is the
dispersal of the
fungus(via spores) to
new habitats.
When new conidia
form they are white
and eventually
become pigmented.
Microbial Eukaryotic Cells






Reproduction (Sexual)
Fungi can reproduce sexually.
An example is bread mold
Rhizopus.
Hyphae called stolons of
opposite mating types (+ & -)
fuse to form a structure called
gametangia
Dipoid zygospore is formed.
Zygospore produces sporandia
which undergo meiosis and
release haploid spores.
Review


Describe the structure of a mold and the functions of
each structure. Include the terms fungal cell,
hyphae, mycelium, and conidia in your description.
Explain fungal asexual and sexual reproduction.
Biology of Fungi


http://www.youtube.com/watch?v=4NO299do_l4
http://www.youtube.com/watch?v=Luxjo0AsbTY&fe
ature=relmfu
Microbial Eukaryotic Cells





Products
Several yeasts, in particular Saccharomyces
cerevisiae, have been widely used in biotechnology.
S. cerevisiae is a simple eukaryotic cell, serving as a
model organism for all eukaryotes.
Fundamental cellular processes such as the cell cycle,,
DNA replication, recombination, cell division, and
metabolism have been studied.
In 1996, S. cerevisiae was announced to be the first
eukaryote to have its genome, consisting of 12
million base pairs, fully sequenced as part of the
Genome project.
Microbial Eukaryotic Cells



Products
S. cerevisiae as a model organism has improved our
understanding of human disease genes.
Genetically engineered yeast and filamentous
fungi have been used in the development of flavors,
fragrances, food colorants, enzymes,
pharmaceuticals (many human proteins), and
solvents.
Lesson 11




MINI -Laboratory :Fungi
Read instructions for making a tease prep.
Sketch a diagram of fungal structures and label.
Please refer to your handout.
Lesson 12





Homework: Review and understand powerpoint and
videos on virus structure, replication, and vectors.
Class: Create 4 work groups and develop review
questions on assigned slides
Class: Present your slides and review questions to the
class.
Work in groups of 4 to create a rap song involving
virus content.
Create and present a rap song about viruses.(See
handout).
Viruses





General Properties
A minute particle containing
nucleic acid, a protein coat,
and sometimes other
macromolecules.
Can exist in extracellular or
intracellular form.
Extracellular –is
metabolically inert.
Intracellular – viral
replication occurs,
Viruses - Genomes



a.
b.
c.
d.
e.

Genomes
Viral genomes are very small (3 to 100
genes)and encode for those functions
that they cannot adapt from their host.
Viral genomes are categorized by the
type of nucleic acid present.
Double stranded DNA
Single stranded DNA
Double stranded RNA
Single stranded RNA
Single stranded RNA that replicates
with a DNA intermediate.
Viral genomes can be linear or
circular.
Viruses - Structure



a.
b.
c.
d.
e.
Virus Structure
Structures of viruses vary widely in
size, shape, and chemical
composition.
Commonalities of structure
Nucleic acid (DNA or RNA)
Capsid- made of one to several
proteins which surrounds nucleic
acid.
Envelope –most animal viruses
have an envelope.
The envelope is composed of a
phopholipid bilayer from the host
and proteins which the virus makes.
Viruses without an envelope are
called naked viruses.
Viruses - Structure





Enzymes
Some viruses contain enzymes.
Bacteriophages have lysozyme
to make a small hole in bacterial
cell wall.
Retroviruses have reverse
transcriptase that transcribes
DNA from their RNA.
Viruses have enzymes because
the cell would not be able to
replicate the viruses with out
them.
Viruses - Replication


a.
b.
c.
d.
e.
Viral Replication
The phases of the
replication process
are
Attachment
Penetration
Synthesis of nucleic
acid and proteins
Assembly
Release
Viruses - Replication





Attachment
Viruses are specific for the
host cells they infect.
Proteins on the outside of
naked or enveloped virus
interact with specific cell
membrane receptors.
If a cell membrane is altered,
the virus cannot infect the cell;
host resistance.
However, viruses protein
mutation enable viruses to
interact with changed
receptors.
Viruses - Replication


a.
b.
c.
Penetration
Three ways a virus can penetrate a cell
membrane:
Membrane Fusion or Hemifusion State:
The cell membrane is punctured and
made to further connect with the
unfolding viral envelope.
Entry Pore formation: An opening is
established through which viral particles
can then enter.
Viral Penetration: The viral capsid or
genome is injected into the host cell's
cytoplasm. (enveloped viruses can
uncoat the envelope at the cell
membrane, cytoplasm, or nuclear
membrane, depending on virus species).
Viruses


http://highered.mcgrawhill.com/sites/0072556781/student_view0/chapte
r18/animation_quiz_1.html
Attachment and penetration
Viruses - Replication




Synthesis of nucleic acids and
proteins - DNA viruses
How viruses synthesize nucleic acids in
the cell depends on the type of nucleic
acid present in the virus.
Double stranded DNA virusIncorporates its DNA into the host
genome and protein synthesis can
begin.
Single stranded DNA virus – A
complimentary DNA strand must be
synthesized in the host because RNA
polymerase requires double stranded
DNA.
Viruses - Replication






Synthesis of nucleic acid and
protein – RNA viruses
RNA viruses need an RNAdependent RNA-polymerase to
replicate their RNA.
Cells do not have this enzyme.
RNA viruses need to code for an
RNA-dependent RNA polymerase.
No viral proteins can be made until
viral messenger RNA is available .
The nature of the RNA in the virus
affects its replication strategy.
Viruses - Replication


a.
b.

Synthesis of nucleic acids and proteins- RNA virus
Single stranded RNA virus – There are 2 types of single
stranded RNA viruses.
Plus-stranded RNA viruses -In these viruses,RNA is the same
sense (direction) as mRNA and it functions as mRNA. This mRNA
can be translated immediately upon infection of the host cell.
Negative-stranded RNA viruses - The virus RNA is negative
sense (complementary to mRNA) and must therefore be copied
into the complementary plus-sense mRNA before proteins can be
made. The virus uses its own RNA polymerase to make the plus
stranded m RNA.
Double-stranded RNA virus - The virus RNA is double stranded
and can’t function as mRNA; these viruses also need to package
an RNA polymerase to make their mRNA after infection of the
host cell.
Viruses - Replication




Synthesis of nucleic acids and proteins – retrovirus.
The single strand of retrovirus RNA serves as a template to make a single strand of DNA
with the virus’ enzyme reverse transcriptase.
A complimentary DNA strand is made and the double stranded DNA is then a template
for mRNA synthesis.
http://highered.mcgrawhill.com/sites/0072495855/student_view0/chapter24/animation__hiv_replication.html
Viruses – Replication




Synthesis of nucleic acids
and proteins
Once mRNA is made proteins
can by synthesized.
Early proteins – are made
first which are necessary for
viral replication.
Late proteins- are then
synthesized such as the viral
coat protein.
Viruses - Replication



Assembly
Viruses self assemble in cells.
Virus self-assembly within host cells has implications
for the study of the origin of life, as it lends
credence to the hypothesis that life could have
started as self-assembling organic molecule
Viruses





Release
Naked virus release
http://faculty.ccbcmd.edu/courses/bio141/lecguid
e/unit3/viruses/release_nv_fl.html
Enveloped virus release
http://highered.mcgrawhill.com/sites/0072556781/student_view0/chapte
r18/animation_quiz_2.html
Viruses - Vector



Viruses as vectors
Vector (in biotechnology) DNA that can be used to
carry and replicate foreign DNA in biotechnology
experiments.
Viruses can serve as vectors. Genes of interest
can be inserted into the viral genome and the genes
of interest will replicate along with the virus.
Viruses - Vector






Viral vectors can be delivery system for gene therapy.
http://www.edu365.cat/aulanet/comsoc/Lab_bio/simu
lacions/GeneTherapy/GeneTherapy.htm
Viruses have potential as delivery systems in gene
therapy because
A. They naturally enter cells.
B. They can integrate in the host cell genome.
C. They are cell specific which would allow for
targeted gene therapy.